Structure modelling based on comparison of hidden Markov models, suggested strong structural similarity with resolved structures of the Escherichia coli and Thermus thermophilus 5'nucleotidase (respective PDBs: 1hO5 and 2Z1a, Fig. 1C).
The long-lived folded states, LF1 and LF2 (Fig. 6A), were dominant in high K+ concentrations and were assigned to the parallel and antiparallel structures respectively, based on comparison with NMR spectroscopic studies of temperature dependence [79].
One common theme is the integration of automatic processing of information (often using controlled vocabularies) that then requires manual oversight and approval by a biocurator, whether it be for gene nomenclature based on orthologs (20) or gene structure based on sequence comparison (21).
Homology detection and structure prediction was based on comparison of Hidden Markov Models (HHpred, http://toolkit.tuebingen.mpg.de/hhpred).
mirCoS can efficiently detect the majority of known miRNAs and predicts an extensive set of hairpin structures based on human-mouse comparisons.
Its structure was assigned as shown based on comparison of its spectroscopic data with those reported in the literature [4].
Structural alignments based on comparisons of 3D structures deposited in the Protein Data Bank (PDB) were obtained from the Dali database [ 70].
Four major approaches have been used successfully, including methods based on comparison of chemical structures, genetic phenocopy, pharmacologic phenocopy and compound affinity.
Conventional cladistic analyses based on comparison of primary structures generally annotate these proteins as PHGPxs, prior to empirical examination of their catalytic mechanisms (for example, see [ 17]).
Structure models of the LdMAcP (residues 26 313) and LdSAcP1 (residues 26 392) were generated with the homology modelling program Swiss Model [ 40] based on comparison with the structure of the human prostatic acid phosphatase (hPAP; residues 1001 1343).
Alternatively, LOX genes are classified based on comparison of LOX primary structures.
